You can also reimport all assets. In my case this method solved the problem.

Here's the method I use:
Close Unity, then go to <Unity directory>\Unity\Editor\Data\UnityExtensions\Unity\GUISystem\ and delete UnityEngine.UI.dll (or delete both files named that) then go into the Editor folder in the above directory and also delete UnityEngine.UI.dll (same name) in that folder (likewise I usually delete both files with that name, for a total of four); then restart Unity, access the project and scene where the problem occurred, but then immediately close it again without doing anything; then go to the Recycle Bin and restore the deleted files - just click on them and right-click then select Restore. Can select all of them at once and then right-click to restore all of them. Then restart Unity and there shouldn't be any errors

In my case this problem was solved by turning off the Google Sync or moving the folder of the project from Google Disc. I think while the synchronization process is going on... the files are allocated by either of them, then (e.g. when files are reserved by the Google Sync) saving process cannot be done and the Unity throws an exception.
1. Try to switch off sync when you are working with this project
2. Move the folder of the project to another place (and sync only after you finish working on this project).
Hope the will help you! :)

i just go to this folder
C:\Program Files\Unity\Editor\Data\UnityExtensions\Unity\GUISystem
and select UnityEngine.UI.dll file & right click & properties & security & Edit & change
all group and Usernames to full control
and close unity again open
and Done

I'm having this bug still on 5.5.0f3... I'm getting this issue for a lot of .dll files (32 to be exact) and have been unable to fix it on my own. Even trying workarounds such as VDESCUBESSEP's method did not work.

Unity 5.3.6p5 still have this problem, plz fix

Thanks for the temporary fix VDESCUBESSEP. That worked for me.

Idk what version this claims it's fixed in, but I am using the most updated version as of today (5.5) and just got this bug.

VDESCUBESSEP 22, 2016 00:25
I have to close Unity, move the content from Data\UnityExtensions extensions folder to a temp place, open Unity, close Unity, move the content back back, open Unity.
The work around lasts until it breaks again...

Asset 'C:/Program Files/Unity/Editor/Data/UnityExtensions/Unity/GUISystem/UnityEngine.UI.dll' is in timestamps but is not known in assetdatabase...

5.5.0f3

I'm only just learning unity and I'm surprised this is such a persistent bug for so many developers, considering Unity is said to be the "go-to" engine for VR, such a glaring bug caught me off-guard.
Looks like it's fixable by deleting the library? For one just learning code, that's nerve wracking

This is embarrassing unity... I've had to completely remove my project and re-clone it from git to get rid of these issues.